Upload Data

Expression Data

An unlabelled peptide expression data file called “pep_edata.csv” was uploaded to pmart. The protein data was rolled-up from peptide data. The column that designates unique molecules was marked as “Protein”. The original scale of the data was log2 and remained unchanged. The value to denote missing data was “NA” and the expression data was not already normalized.

Biomolecule Information

An associated biomolecule information file was also uploaded called pep_emeta.csv and the protein identifier column was designated as Protein.

Sample Information

An associated sample information file was also uploaded called “pep_fdata.csv”. Trimmed sample names were not used. The column in the sample information file which indicates sample names was designated as “SampleID”.

Group Samples

Grouping Information

This table summarizes all the user specified main effects or covariates in pmart. The “Selected Column Name” denotes the name of the column in the sample information file assigned as a main effect or covariate.

Main Effect or Covariate Selected Column Name
First Main Effect Condition
Second Main Effect None selected
First Covariate None selected
Second Covariate None selected

Number of Samples per Main Effects

Data Summary

Summary Table

The first column in the table below denotes a property of the peptide data, and the “Data” column states that property’s value.

Data
Class proData
Unique SampleIDs (f_data) 11
Unique Proteins (e_data) 1736
Unique Proteins (e_meta) NA
Missing Observations 13741
Proportion Missing 0.72

Missing Value Table

In the table below, the first column denotes the sample and the second is the missing number of observations. The third column represents the second as a percentage of the total number of observations for that sample.

Missing Observations Proportion Missing
Infection1 1151 0.663
Infection2 1127 0.649
Infection3 1308 0.753
Infection4 1366 0.787
Infection6 1293 0.745
Infection7 1248 0.719
Infection8 1568 0.903
Infection9 1511 0.870
Mock1 1079 0.622
Mock2 1049 0.604
Mock3 1041 0.600

Filters were not applied.

Summary of Applied Filters

Molecule Filter

Molecule filters were not applied to the data.

CV Filter

CV filters were not applied to the data.

imd-ANOVA Filter

imd-ANOVA filters were not applied to the data.

Proteomics Filter

Proteomics filters were not applied to the data.

rMD Filter

rMD filters were not applied to the data.

Custom Filter

Custom filters were not applied to the data.

Normalization

Peptide data was normalized.

SPANS

SPANS was run to determine optimum normalization parameters.

Manual

Manual normalization was not used to normalize the data.

Protein Roll-Up

Protein Roll-Up was conducted.

Protein quantification was conducted with the rrollup method and was centered with the median. The quantile cutoff was restricted to 0.

Statistical Analysis

The statistical analysis step was run.

The following groups were compared: Mock_vs_Infection. Reported below are the parameters used in the statistical analysis, followed by the number of siginificant biomolecules for each comparison.

Attribute Value
Test Method anova
Multiple Comparison Adjustment holm
Significance Threshold 0.05
Comparison Up_total Down_total Up_anova Down_anova Up_gtest Down_gtest
Mock_vs_Infection Mock_vs_Infection 718 328 718 328 0 0